Multiple sequence alignment - TraesCS4D01G155200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G155200 chr4D 100.000 2399 0 0 1 2399 207069171 207066773 0 4431
1 TraesCS4D01G155200 chr1D 94.604 2409 112 11 1 2399 254434091 254436491 0 3712
2 TraesCS4D01G155200 chr1D 93.190 1718 93 14 693 2399 51872191 51870487 0 2503
3 TraesCS4D01G155200 chr5D 94.562 2409 111 9 1 2399 6177857 6175459 0 3705
4 TraesCS4D01G155200 chr5D 94.437 1492 67 8 920 2399 512410158 512411645 0 2281
5 TraesCS4D01G155200 chr5D 95.024 1447 69 3 1 1447 503290417 503291860 0 2270
6 TraesCS4D01G155200 chr2D 94.401 2411 111 12 1 2399 638423566 638425964 0 3683
7 TraesCS4D01G155200 chr4B 93.657 2412 131 9 1 2399 308680709 308678307 0 3587
8 TraesCS4D01G155200 chr4A 92.813 2407 151 14 1 2396 309490740 309488345 0 3467
9 TraesCS4D01G155200 chr3D 90.532 2408 184 14 1 2399 235617963 235620335 0 3144
10 TraesCS4D01G155200 chr2A 93.451 2046 107 15 202 2229 32525820 32527856 0 3011


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G155200 chr4D 207066773 207069171 2398 True 4431 4431 100.000 1 2399 1 chr4D.!!$R1 2398
1 TraesCS4D01G155200 chr1D 254434091 254436491 2400 False 3712 3712 94.604 1 2399 1 chr1D.!!$F1 2398
2 TraesCS4D01G155200 chr1D 51870487 51872191 1704 True 2503 2503 93.190 693 2399 1 chr1D.!!$R1 1706
3 TraesCS4D01G155200 chr5D 6175459 6177857 2398 True 3705 3705 94.562 1 2399 1 chr5D.!!$R1 2398
4 TraesCS4D01G155200 chr5D 512410158 512411645 1487 False 2281 2281 94.437 920 2399 1 chr5D.!!$F2 1479
5 TraesCS4D01G155200 chr5D 503290417 503291860 1443 False 2270 2270 95.024 1 1447 1 chr5D.!!$F1 1446
6 TraesCS4D01G155200 chr2D 638423566 638425964 2398 False 3683 3683 94.401 1 2399 1 chr2D.!!$F1 2398
7 TraesCS4D01G155200 chr4B 308678307 308680709 2402 True 3587 3587 93.657 1 2399 1 chr4B.!!$R1 2398
8 TraesCS4D01G155200 chr4A 309488345 309490740 2395 True 3467 3467 92.813 1 2396 1 chr4A.!!$R1 2395
9 TraesCS4D01G155200 chr3D 235617963 235620335 2372 False 3144 3144 90.532 1 2399 1 chr3D.!!$F1 2398
10 TraesCS4D01G155200 chr2A 32525820 32527856 2036 False 3011 3011 93.451 202 2229 1 chr2A.!!$F1 2027

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
276 277 0.254444 TCTAGGTGGGGGAGTAGGGA 60.254 60.000 0.0 0.0 0.0 4.20 F
649 656 1.303282 GGCGGAGAAGGGTGGATTT 59.697 57.895 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 1171 0.984995 GCCTAAAGGAGTGTGGGTCT 59.015 55.000 0.0 0.0 37.39 3.85 R
1534 1550 4.097418 TCGAATCCCTCTCTCTCCTTTTT 58.903 43.478 0.0 0.0 0.00 1.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.101249 AGGTTCTAACACGTGGAAACGA 59.899 45.455 21.57 5.88 36.85 3.85
75 76 1.133730 ACCAAGAAACCACCGGCTTTA 60.134 47.619 0.00 0.00 0.00 1.85
83 84 3.015516 CACCGGCTTTACTTGGTGT 57.984 52.632 0.00 0.00 45.34 4.16
95 96 0.896940 CTTGGTGTGCTGGGAATGCT 60.897 55.000 0.00 0.00 0.00 3.79
166 167 3.556423 GCCGGATTAATCGTATTCTGGGT 60.556 47.826 5.05 0.00 36.93 4.51
200 201 4.167319 ACCTATTTGAAGTGGCCCATTTT 58.833 39.130 0.00 0.00 0.00 1.82
227 228 4.142315 CCAGAAAAGCCCATGTATGAACAG 60.142 45.833 0.00 0.00 39.49 3.16
276 277 0.254444 TCTAGGTGGGGGAGTAGGGA 60.254 60.000 0.00 0.00 0.00 4.20
338 340 4.259356 GGCGTACTTCACCTAATTTCCTT 58.741 43.478 0.00 0.00 0.00 3.36
373 375 2.997980 TCGGTGGCATTTATCACATGT 58.002 42.857 0.00 0.00 35.74 3.21
587 593 8.705594 TGTTAGAAAAATTACCAATTTGACCCA 58.294 29.630 0.00 0.00 40.05 4.51
633 640 9.582431 GGTTATTTACTAAAATCTCCTTTTGGC 57.418 33.333 0.00 0.00 38.49 4.52
649 656 1.303282 GGCGGAGAAGGGTGGATTT 59.697 57.895 0.00 0.00 0.00 2.17
800 807 8.251721 GTCTGGAGAAGCTTACTTGTCTTATAA 58.748 37.037 0.00 0.00 43.85 0.98
870 877 9.502091 GTATGGTTCAATAATACAGCTTATCCA 57.498 33.333 0.00 0.00 0.00 3.41
892 899 2.041216 AGTGAGTTTTATGGACCCACCC 59.959 50.000 0.00 0.00 38.00 4.61
954 961 2.744760 AGAGACTAGCATCTTGGAGCA 58.255 47.619 0.00 0.00 0.00 4.26
982 989 1.488705 ATCCGCTCAAGGACCCACAA 61.489 55.000 0.00 0.00 44.07 3.33
1077 1084 2.271800 CTTCGTGCTCCATGGTTAGAC 58.728 52.381 12.58 3.92 0.00 2.59
1163 1171 6.208988 AGAACGACACTCAGCAGAATATAA 57.791 37.500 0.00 0.00 0.00 0.98
1171 1179 4.716784 ACTCAGCAGAATATAAGACCCACA 59.283 41.667 0.00 0.00 0.00 4.17
1205 1213 1.540267 TTAAATTCTGTGGGTGGCGG 58.460 50.000 0.00 0.00 0.00 6.13
1242 1250 8.964476 TCAATTCAGTTAATTATGTCTCTCCC 57.036 34.615 0.00 0.00 35.54 4.30
1244 1252 9.177608 CAATTCAGTTAATTATGTCTCTCCCAA 57.822 33.333 0.00 0.00 35.54 4.12
1378 1386 5.356882 TCGTGATTTGGAACATGTTCTTC 57.643 39.130 31.81 23.31 39.30 2.87
1405 1413 9.588096 ACATGAACCCTCTTAACTAAGATTTTT 57.412 29.630 0.00 0.00 41.12 1.94
1477 1488 0.179034 AGCCGAGCCATTCATTCCTC 60.179 55.000 0.00 0.00 0.00 3.71
1648 1664 8.326765 TCCACAGCCTAATCCTTATTTTACTA 57.673 34.615 0.00 0.00 0.00 1.82
1824 1845 3.048600 TCTTCTCACCCCCATATCCAAG 58.951 50.000 0.00 0.00 0.00 3.61
1829 1850 4.165372 TCTCACCCCCATATCCAAGTAAAC 59.835 45.833 0.00 0.00 0.00 2.01
1834 1855 4.277476 CCCCATATCCAAGTAAACAAGCA 58.723 43.478 0.00 0.00 0.00 3.91
1945 1977 6.103205 AGTGGGGGATCAAATATGTAGTCAAT 59.897 38.462 0.00 0.00 0.00 2.57
1974 2006 4.298626 TGATGGTAGCTTGGAGGATTAGT 58.701 43.478 0.00 0.00 0.00 2.24
2066 2098 4.288626 TGTACCCCTTGTATTTGCTTCTCT 59.711 41.667 0.00 0.00 0.00 3.10
2302 2337 8.700051 TGCTAGCTCTTCTCTTTCAGTATTATT 58.300 33.333 17.23 0.00 0.00 1.40
2335 2370 7.773489 TTCCCATTAGAATGTTCATTGACAA 57.227 32.000 2.63 0.00 34.60 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 1.181098 GCATTCCCAGCACACCAAGT 61.181 55.000 0.00 0.00 0.00 3.16
83 84 3.711190 TGATAAGTCTAGCATTCCCAGCA 59.289 43.478 0.00 0.00 0.00 4.41
166 167 4.214986 TCAAATAGGTTCATTGCTCCGA 57.785 40.909 0.00 0.00 0.00 4.55
200 201 2.969821 ACATGGGCTTTTCTGGTACA 57.030 45.000 0.00 0.00 0.00 2.90
227 228 4.149598 AGTGTGGAAGTAAAATCAACCCC 58.850 43.478 0.00 0.00 0.00 4.95
264 265 1.075151 CCTCTGTCCCTACTCCCCC 60.075 68.421 0.00 0.00 0.00 5.40
276 277 7.093245 GGAAAAGTATCTAGAACTTCCCTCTGT 60.093 40.741 15.90 2.46 36.17 3.41
338 340 1.248785 ACCGAAGCCTAAGACTGCGA 61.249 55.000 0.00 0.00 38.54 5.10
373 375 2.634940 CAAGAGTCTCAGGTCCCAGAAA 59.365 50.000 1.94 0.00 0.00 2.52
555 561 6.860790 TTGGTAATTTTTCTAACATCCCCC 57.139 37.500 0.00 0.00 0.00 5.40
556 562 9.161629 CAAATTGGTAATTTTTCTAACATCCCC 57.838 33.333 0.00 0.00 38.97 4.81
557 563 9.936759 TCAAATTGGTAATTTTTCTAACATCCC 57.063 29.630 0.00 0.00 38.97 3.85
633 640 3.689649 CACTAAAAATCCACCCTTCTCCG 59.310 47.826 0.00 0.00 0.00 4.63
679 686 0.324183 CCCAACCATACATGCCCACA 60.324 55.000 0.00 0.00 0.00 4.17
800 807 8.706322 ACCAAAGACAGATAAACCAACTAAAT 57.294 30.769 0.00 0.00 0.00 1.40
809 816 7.527457 AGCGATAAAACCAAAGACAGATAAAC 58.473 34.615 0.00 0.00 0.00 2.01
870 877 3.499745 GGGTGGGTCCATAAAACTCACTT 60.500 47.826 6.26 0.00 45.53 3.16
892 899 2.464682 CTTGAGAAGCTTCTGGCCG 58.535 57.895 33.07 14.27 43.05 6.13
940 947 3.018856 CCACATTTGCTCCAAGATGCTA 58.981 45.455 0.00 0.00 0.00 3.49
944 951 2.905415 TCCCACATTTGCTCCAAGAT 57.095 45.000 0.00 0.00 0.00 2.40
954 961 1.683011 CCTTGAGCGGATCCCACATTT 60.683 52.381 6.06 0.00 0.00 2.32
982 989 9.269453 GGAACGCATTAGATATTTACCTAAACT 57.731 33.333 0.00 0.00 0.00 2.66
1022 1029 5.643777 CGCATAGTTTCCCCTCCAAATATAG 59.356 44.000 0.00 0.00 0.00 1.31
1026 1033 2.025321 ACGCATAGTTTCCCCTCCAAAT 60.025 45.455 0.00 0.00 0.00 2.32
1123 1131 3.749088 CGTTCTTGCCAAGGTTGTATGTA 59.251 43.478 4.30 0.00 0.00 2.29
1163 1171 0.984995 GCCTAAAGGAGTGTGGGTCT 59.015 55.000 0.00 0.00 37.39 3.85
1171 1179 7.391833 CACAGAATTTAAAGAGCCTAAAGGAGT 59.608 37.037 0.00 0.00 37.39 3.85
1222 1230 8.383175 ACTTTTGGGAGAGACATAATTAACTGA 58.617 33.333 0.00 0.00 0.00 3.41
1378 1386 8.567285 AAATCTTAGTTAAGAGGGTTCATGTG 57.433 34.615 7.57 0.00 44.67 3.21
1477 1488 9.816354 TTTTGTCCCTTTTCTTTCTTTCATAAG 57.184 29.630 0.00 0.00 0.00 1.73
1523 1539 9.460019 CCTCTCTCTCCTTTTTCTTATTGAATT 57.540 33.333 0.00 0.00 34.24 2.17
1534 1550 4.097418 TCGAATCCCTCTCTCTCCTTTTT 58.903 43.478 0.00 0.00 0.00 1.94
1563 1579 8.544687 AAACCGGTATAGTTCTAGGAACTATT 57.455 34.615 26.99 16.50 41.70 1.73
1648 1664 8.871629 TTATATGGTTGTGTTCCATTTGTAGT 57.128 30.769 2.79 0.00 42.24 2.73
1747 1768 6.842437 AGCGGATCTTGTATCTGTGTATAT 57.158 37.500 0.00 0.00 0.00 0.86
1945 1977 6.489603 TCCTCCAAGCTACCATCAAATAAAA 58.510 36.000 0.00 0.00 0.00 1.52
1987 2019 5.055812 TGCAAAAACAGCTAATTGGAAAGG 58.944 37.500 0.00 0.00 0.00 3.11
2105 2137 9.331466 AGACTAGTCCAATCCATAATGATGTAT 57.669 33.333 19.38 0.00 0.00 2.29
2234 2269 9.031360 TGCGTTTTAATACATCTCACTATTCTC 57.969 33.333 0.00 0.00 0.00 2.87


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.